annotate test-data/tRNA.rnaz @ 0:e123d5c6f489 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty

############################  RNAz 2.1  ##############################

 Sequences: 4
 Columns: 73
 Reading direction: forward
 Mean pairwise identity:  80.82
 Shannon entropy: 0.31118
 G+C content: 0.54795
 Mean single sequence MFE: -27.20
 Consensus MFE: -26.50
 Energy contribution: -23.63
 Covariance contribution:  -2.87
 Combinations/Pair:   1.43
 Mean z-score:  -1.82
 Structure conservation index:   0.97
 Background model: dinucleotide
 Decision model: sequence based alignment quality
 SVM decision value:   2.15
 SVM RNA-class probability: 0.984068
 Prediction: RNA

######################################################################

>sacCer1.chr4 1352453 73 - 1531914
GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score =  -2.35, R)
>sacBay.contig_465 14962 73 - 57401
GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score =  -2.35, R)
>sacKlu.Contig1694 137 73 + 4878
GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU
(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score =  -1.34, R)
>sacCas.Contig128 258 73 + 663
GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA
(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score =  -1.22, R)
>consensus
GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 +  -2.87) 

############################  RNAz 2.1  ##############################

 Sequences: 4
 Columns: 73
 Reading direction: reverse
 Mean pairwise identity:  80.82
 Shannon entropy: 0.31118
 G+C content: 0.54795
 Mean single sequence MFE: -24.15
 Consensus MFE: -26.66
 Energy contribution: -23.35
 Covariance contribution:  -3.31
 Combinations/Pair:   1.48
 Mean z-score:  -1.79
 Structure conservation index:   1.10
 Background model: dinucleotide
 Decision model: sequence based alignment quality
 SVM decision value:   2.58
 SVM RNA-class probability: 0.992927
 Prediction: RNA

######################################################################

>sacCer1.chr4 1352453 73 + 1531914
AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score =  -2.22, R)
>sacBay.contig_465 14962 73 + 57401
AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score =  -2.22, R)
>sacKlu.Contig1694 137 73 - 4878
AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
.......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score =  -1.87, R)
>sacCas.Contig128 258 73 - 663
UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC
.(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score =  -0.83, R)
>consensus
AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 +  -3.31) 

############################  RNAz 2.1  ##############################

 Sequences: 4
 Columns: 73
 Reading direction: forward
 Mean pairwise identity:  80.82
 Shannon entropy: 0.31118
 G+C content: 0.54795
 Mean single sequence MFE: -24.15
 Consensus MFE: -26.66
 Energy contribution: -23.35
 Covariance contribution:  -3.31
 Combinations/Pair:   1.48
 Mean z-score:  -1.79
 Structure conservation index:   1.10
 Background model: dinucleotide
 Decision model: sequence based alignment quality
 SVM decision value:   2.58
 SVM RNA-class probability: 0.992927
 Prediction: RNA

######################################################################

>sacCer1.chr4 1352453 73 + 1531914
AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score =  -2.22, R)
>sacBay.contig_465 14962 73 + 57401
AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) ( -24.70, z-score =  -2.22, R)
>sacKlu.Contig1694 137 73 - 4878
AGCCCUGUAGGGGGCUCGAACCCCUAGCCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
.......((((((.......))))))((((((((((.....)))))..((((........))))....))))) ( -25.20, z-score =  -1.87, R)
>sacCas.Contig128 258 73 - 663
UGCUCCAGGGGAGGUUCGAACUCUCGACCUUCAGAUUAUGAGACUGACGCUCUUCCGACUGAGCUACUGAAGC
.(((.(((.((((((.(((....)))))))))................((((........))))..))).))) ( -22.00, z-score =  -0.83, R)
>consensus
AGCCCUGUAGGGGGCUCGAACCCCUAACCUUAUGAUUAAGAGUCAUACGCGCUACCGAUUGCGCCAACAAGGC
.(((.((((((((.......))))).....((((((.....)))))).((((........))))..))).))) (-26.66 = -23.35 +  -3.31) 

############################  RNAz 2.1  ##############################

 Sequences: 4
 Columns: 73
 Reading direction: reverse
 Mean pairwise identity:  80.82
 Shannon entropy: 0.31118
 G+C content: 0.54795
 Mean single sequence MFE: -27.20
 Consensus MFE: -26.50
 Energy contribution: -23.63
 Covariance contribution:  -2.87
 Combinations/Pair:   1.43
 Mean z-score:  -1.82
 Structure conservation index:   0.97
 Background model: dinucleotide
 Decision model: sequence based alignment quality
 SVM decision value:   2.15
 SVM RNA-class probability: 0.984068
 Prediction: RNA

######################################################################

>sacCer1.chr4 1352453 73 - 1531914
GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score =  -2.35, R)
>sacBay.contig_465 14962 73 - 57401
GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
(((((((.(((((........))))...((((.((((....))))))))(((((....)))))).))))))). ( -29.20, z-score =  -2.35, R)
>sacKlu.Contig1694 137 73 + 4878
GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGCCCCCUACAGGGCU
(((((((.(((((........)))).(((((.......)))))......(((((....)))))).))))))). ( -27.20, z-score =  -1.34, R)
>sacCas.Contig128 258 73 + 663
GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAACCUCCCCUGGAGCA
(((((((..((((........)))).((((.........))))((((((......)).))))...))))))). ( -23.20, z-score =  -1.22, R)
>consensus
GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGCCCCCUACAGGGCU
(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.50 = -23.63 +  -2.87)